12-5-2021
Introduction
Study
Sanctuary et al., 2019: Pilot study of probiotic/colostrum supplementation on gut function in children with autism and gastrointestinal symptoms
- Prebiotic (Bovine Milk Oligosaccharides) or synbiotic (BMO + B. infantis) treatment
- Autism symptoms
- Gastrointestinal symptoms
- Metabolites from fecal, urine, and serum samples
- Immune cell populations in blood
- Microbiota of fecal samples
Data
Study design:
Data
Excel file with six sheets:
Methods
Tidying data
- Align column names
- Change entries with typos
- Assign NAs
- Remove undesired and empty columns
- Filter out redundancy
Tidying data
immune_microbiota data issue:
## # A tibble: 16 x 5 ## Subject Treatment Arm IL13_CD4_Pre IL13_CD4_Post ## <dbl> <chr> <dbl> <dbl> <dbl> ## 1 202 Pre 1 3.57 1.41 ## 2 205 Pre 1 1.97 2.9 ## 3 208 Pre 1 NA NA ## 4 210 Pre 1 0.7 1.13 ## 5 204 Pre 2 7.11 1.68 ## 6 207 Pre 2 2.89 1.88 ## 7 211 Pre 2 7.75 2.59 ## 8 212 Pre 2 3.98 3.86 ## 9 204 Syn 1 4.02 1.74 ## 10 207 Syn 1 3.25 1.45 ## 11 211 Syn 1 4.17 2.75 ## 12 212 Syn 1 3.48 3.27 ## 13 202 Syn 2 2.68 1.41 ## 14 205 Syn 2 2.87 0.9 ## 15 208 Syn 2 NA NA ## 16 210 Syn 2 0.9 0.76
Tidying data
GI_behavior data issue:
## # A tibble: 16 x 6 ## Subject Treatment Arm Order Stool_Freq_Pre Stool_Norm_Pre ## <dbl> <chr> <dbl> <chr> <dbl> <dbl> ## 1 202 Pre 1 PS NA NA ## 2 202 Syn 2 PS NA NA ## 3 204 Pre 2 SP NA NA ## 4 204 Syn 1 SP NA NA ## 5 205 Pre 1 PS NA NA ## 6 205 Syn 2 PS NA NA ## 7 207 Pre 2 SP 3.47 0 ## 8 207 Syn 1 SP 4.75 0 ## 9 208 Pre 1 PS NA NA ## 10 208 Syn 2 PS 0.333 0.75 ## 11 210 Pre 1 PS 0.857 0.4 ## 12 210 Syn 2 PS 0.824 0.357 ## 13 211 Pre 2 SP 0.810 0.294 ## 14 211 Syn 1 SP 0.769 0.5 ## 15 212 Pre 2 SP 1.4 0.286 ## 16 212 Syn 1 SP 1.21 0.294
Tidying data
Data from stool log excluded:
## spec_tbl_df[,24] [16 × 24] (S3: spec_tbl_df/tbl_df/tbl/data.frame) ## $ Subject : num [1:16] 202 202 204 204 205 205 207 207 208 208 ... ## $ Treatment : chr [1:16] "Pre" "Syn" "Pre" "Syn" ... ## $ Arm : num [1:16] 1 2 2 1 1 2 2 1 1 2 ... ## $ Order : chr [1:16] "PS" "PS" "SP" "SP" ... ## $ Stool_Freq_Pre : num [1:16] NA NA NA NA NA ... ## $ Stool_Norm_Pre : num [1:16] NA NA NA NA NA NA 0 0 NA 0.75 ... ## $ Stool_Hard_Pre : num [1:16] NA NA NA NA NA ... ## $ Stool_Soft_Pre : num [1:16] NA NA NA NA NA ... ## $ Stool_Freq_D123: num [1:16] 0.667 0.667 0 1 2 ... ## $ Stool_Freq_W1 : num [1:16] 0.571 0.286 0.571 0.714 2.143 ... ## $ Stool_Freq_W5 : num [1:16] 0.5 0.286 1 1 2.143 ... ## $ Stool_Freq_D835: num [1:16] 0.368 0.227 1.091 0.789 2.182 ... ## $ Stool_Norm_D123: num [1:16] 0 0 NA 0 0.2 0.4 0 0 0 NA ... ## $ Stool_Norm_W1 : num [1:16] 0 0 0 0.2 0.214 ... ## $ Stool_Norm_W5 : num [1:16] 0.5 0 0.571 0.667 0.6 ... ## $ Stool_Norm_D835: num [1:16] 0.286 0.1 0.833 0.2 0.429 ... ## $ Stool_Hard_D123: num [1:16] 1 1 NA 0 0.2 0.4 0 0 0 NA ... ## $ Stool_Hard_W1 : num [1:16] 1 1 0.75 0 0.286 ... ## $ Stool_Hard_W5 : num [1:16] 0.5 0.8 0.143 0 0.133 ... ## $ Stool_Hard_D835: num [1:16] 0.1111 0.5714 0.0385 0.381 0.1692 ... ## $ Stool_Soft_D123: num [1:16] 0 0 NA 0.667 0 ... ## $ Stool_Soft_W1 : num [1:16] 0 0 0.25 0.4 0.0714 ... ## $ Stool_Soft_W5 : num [1:16] 0 0 0 0 0.0667 ... ## $ Stool_Soft_D835: num [1:16] 0 0 0 0.2381 0.0769 ... ## - attr(*, "spec")= ## .. cols( ## .. Subject = col_double(), ## .. Treatment = col_character(), ## .. Arm = col_double(), ## .. Order = col_character(), ## .. Stool_Freq_Pre = col_double(), ## .. Stool_Norm_Pre = col_double(), ## .. Stool_Hard_Pre = col_double(), ## .. Stool_Soft_Pre = col_double(), ## .. Stool_Freq_D123 = col_double(), ## .. Stool_Freq_W1 = col_double(), ## .. Stool_Freq_W5 = col_double(), ## .. Stool_Freq_D835 = col_double(), ## .. Stool_Norm_D123 = col_double(), ## .. Stool_Norm_W1 = col_double(), ## .. Stool_Norm_W5 = col_double(), ## .. Stool_Norm_D835 = col_double(), ## .. Stool_Hard_D123 = col_double(), ## .. Stool_Hard_W1 = col_double(), ## .. Stool_Hard_W5 = col_double(), ## .. Stool_Hard_D835 = col_double(), ## .. Stool_Soft_D123 = col_double(), ## .. Stool_Soft_W1 = col_double(), ## .. Stool_Soft_W5 = col_double(), ## .. Stool_Soft_D835 = col_double() ## .. )
Joining data
full_join() of all tables into final_data:
## spec_tbl_df[,670] [32 × 670] (S3: spec_tbl_df/tbl_df/tbl/data.frame) ## $ #SampleID : chr [1:32] "Aut16" "Aut15" "Aut18" "Aut17" ... ## $ Subject : num [1:32] 202 202 202 202 204 204 204 204 205 205 ... ## $ Sample : chr [1:32] "202_v1" "202_v2" "202_v3" "202_v4" ... ## $ Visit : num [1:32] 1 2 3 4 1 2 3 4 1 2 ... ## $ Timing : chr [1:32] "Pre" "Post" "Pre" "Post" ... ## $ Treatment : chr [1:32] "Pre" "Pre" "Syn" "Syn" ... ## $ Mixer : chr [1:32] NA "non-probiotic" NA "non-probiotic" ... ## $ Arm : num [1:32] 1 1 2 2 1 1 2 2 1 1 ... ## $ Order : chr [1:32] "PS" "PS" "PS" "PS" ... ## $ Run : num [1:32] 1 1 1 1 1 1 1 1 1 1 ... ## $ 1,3-Dihydroxyacetone_fecal : num [1:32] 1.288 1.044 1.047 1.079 0.723 ... ## $ 2-Oxocaproate_fecal : num [1:32] 1.88 5.2 5.33 5.51 8.42 ... ## $ 3-Phenylpropionate_fecal : num [1:32] 0 0 0 0 7.73 ... ## $ 4-Hydroxyphenylacetate_fecal : num [1:32] 1.74 1.76 2.44 1.98 1.08 ... ## $ Acetate_fecal : num [1:32] 588 1004 1752 907 1605 ... ## $ Alanine_fecal : num [1:32] 35.3 30.1 49.5 43.2 22.2 ... ## $ Arabinose_fecal : num [1:32] 4.09 4.23 5.96 2.23 2.15 ... ## $ Arginine_fecal : num [1:32] 11.05 2.35 6.09 3.8 0 ... ## $ Aspartate_fecal : num [1:32] 24.7 15.7 40.8 30.4 12.9 ... ## $ Butyrate_fecal : num [1:32] 137 139 343 210 457 ... ## $ DL-methionine-sulfoxide_fecal : num [1:32] 1.131 0.731 0.825 1.005 0.523 ... ## $ Ethanol_fecal : num [1:32] 1.84 1.98 6.72 1.68 33.69 ... ## $ Formate_fecal : num [1:32] 3.78 4.14 6.28 3.15 3.83 ... ## $ Fumarate_fecal : num [1:32] 4.4 4.07 5.49 3.4 2.17 ... ## $ Galactose_fecal : num [1:32] 3.25 5.45 6.44 7.62 5.4 ... ## $ Glucose_fecal : num [1:32] 22.2 20.9 69.4 11.3 33.1 ... ## $ Glutamate_fecal : num [1:32] 153 123 134 145 152 ... ## $ Glycerol_fecal : num [1:32] 36.9 51.1 83.2 40.7 46.2 ... ## $ Glycine_fecal : num [1:32] 17.6 11.2 24.7 20.9 11.4 ... ## $ Hypoxanthine_fecal : num [1:32] 2.44 5.2 6.5 4.76 5.4 ... ## $ Isobutyrate_fecal : num [1:32] 22.2 44.2 44.8 48.6 57.3 ... ## $ Isoleucine_fecal : num [1:32] 13.15 9.71 16.3 16.14 7.46 ... ## $ Isovalerate_fecal : num [1:32] 19.7 31.4 27.8 44.8 52.6 ... ## $ Leucine_fecal : num [1:32] 18.77 20.44 25.31 21.46 7.73 ... ## $ Lysine_fecal : num [1:32] 37.4 32.7 37.9 40 16.7 ... ## $ Malonate_fecal : num [1:32] 4.14 21.78 22.93 16.18 9.57 ... ## $ Maltose_fecal : num [1:32] 0 0 0 0 9.47 ... ## $ Methanol_fecal : num [1:32] 4.75 3.45 19.79 3.09 8.77 ... ## $ Methionine_fecal : num [1:32] 9.38 8 16.14 11.01 4.66 ... ## $ Methylamine_fecal : num [1:32] 2.45 3.55 14.4 3.56 4.59 ... ## $ N-Acetylglutamate_fecal : num [1:32] 4.85 3.22 5.58 3.5 8.43 ... ## $ Nicotinate_fecal : num [1:32] 6.52 5.43 5.77 3.38 4.06 ... ## $ Ornithine_fecal : num [1:32] 1.08 4.72 4.82 3.28 2.14 ... ## $ Phenylacetate_fecal : num [1:32] 11.2 20.8 16.9 26.2 30.3 ... ## $ Phenylalanine_fecal : num [1:32] 9.13 7.81 13.99 10.61 3.86 ... ## $ Proline_fecal : num [1:32] 13.31 6.98 8.98 5.11 8.1 ... ## $ Propionate_fecal : num [1:32] 194 337 426 272 370 ... ## $ Ribose_fecal : num [1:32] 22.78 24.86 23.31 27.23 7.99 ... ## $ Serine_fecal : num [1:32] 10.77 12.86 14.62 14.16 9.17 ... ## $ Succinate_fecal : num [1:32] 6.12 7.26 930.22 18.37 5.31 ... ## $ Taurine_fecal : num [1:32] 0 0 0 0 0 ... ## $ Threonine_fecal : num [1:32] 10.49 9.62 13.26 14.04 6.45 ... ## $ Thymine_fecal : num [1:32] 1.32 1.71 1.4 2.93 1.09 ... ## $ Tryptophan_fecal : num [1:32] 2.384 1.931 2.632 2.423 0.908 ... ## $ Tyrosine_fecal : num [1:32] 13.97 10.68 19.09 16.98 6.22 ... ## $ Uracil_fecal : num [1:32] 5.41 5.74 7.39 8.14 4.63 ... ## $ Uridine_fecal : num [1:32] 0.661 1.009 1.554 0.798 0 ... ## $ Valerate_fecal : num [1:32] 30.6 45.8 52.1 60.2 89.7 ... ## $ Valine_fecal : num [1:32] 17.4 13 22.3 21.6 10.4 ... ## $ p-Cresol_fecal : num [1:32] 7.26 11.12 10.15 15.63 11.7 ... ## $ LinkerPrimerSequence : chr [1:32] "GTGTGCCAGCMGCCGCGGTAA" "GTGTGCCAGCMGCCGCGGTAA" "GTGTGCCAGCMGCCGCGGTAA" "GTGTGCCAGCMGCCGCGGTAA" ... ## $ Unassigned;Other : num [1:32] 0.0212 0.0199 0.0136 0.0218 0.0157 ... ## $ k__Archaea;p__Euryarchaeota : num [1:32] 0.000226 0 0.000418 0.000445 0.023963 ... ## $ k__Bacteria;p__Acidobacteria : num [1:32] 0 0 0.000209 0 0 ... ## $ k__Bacteria;p__Actinobacteria : num [1:32] 0.1249 0.0346 0.0578 0.0871 0.0067 ... ## $ k__Bacteria;p__Aquificae : num [1:32] 0 0 0 0 0 0 0 0 0 0 ... ## $ k__Bacteria;p__Bacteroidetes : num [1:32] 0.14 0.154 0.188 0.157 0.172 ... ## $ k__Bacteria;p__Chloroflexi : num [1:32] 0 0 0 0 0.000258 ... ## $ k__Bacteria;p__Cyanobacteria : num [1:32] 0 0 0.001879 0.000445 0.000258 ... ## $ k__Bacteria;p__Elusimicrobia : num [1:32] 0 0 0 0 0 0 0 0 0 0 ... ## $ k__Bacteria;p__Firmicutes : num [1:32] 0.709 0.785 0.729 0.731 0.758 ... ## $ k__Bacteria;p__Fusobacteria : num [1:32] 0 0 0 0 0 0 0 0 0 0 ... ## $ k__Bacteria;p__Lentisphaerae : num [1:32] 0 0 0 0 0.000515 ... ## $ k__Bacteria;p__Proteobacteria : num [1:32] 0.00316 0.00287 0.00355 0.002 0.01237 ... ## $ k__Bacteria;p__Spirochaetes : num [1:32] 0 0 0.000418 0 0 ... ## $ k__Bacteria;p__Synergistetes : num [1:32] 0 0 0 0 0 0 0 0 0 0 ... ## $ k__Bacteria;p__TM7 : num [1:32] 0 0 0.000418 0 0 ... ## $ k__Bacteria;p__Tenericutes : num [1:32] 0 0 0.00188 0 0.00799 ... ## $ k__Bacteria;p__Verrucomicrobia : num [1:32] 0.001356 0.003411 0.002715 0.000445 0.002061 ... ## $ k__Bacteria;p__[Thermi] : num [1:32] 0 0 0 0 0 0 0 0 0 0 ... ## $ Unassigned;Other;Other : num [1:32] 0.0212 0.0199 0.0136 0.0218 0.0157 ... ## $ k__Archaea;p__Euryarchaeota;c__Methanobacteria : num [1:32] 0.000226 0 0.000418 0.000445 0.023963 ... ## $ k__Archaea;p__Euryarchaeota;c__Thermoplasmata : num [1:32] 0 0 0 0 0 0 0 0 0 0 ... ## $ k__Bacteria;p__Acidobacteria;c__[Chloracidobacteria] : num [1:32] 0 0 0.000209 0 0 ... ## $ k__Bacteria;p__Actinobacteria;c__Actinobacteria : num [1:32] 0.068459 0.023694 0.032992 0.067141 0.000515 ... ## $ k__Bacteria;p__Actinobacteria;c__Coriobacteriia : num [1:32] 0.05648 0.01095 0.02485 0.01979 0.00618 ... ## $ k__Bacteria;p__Actinobacteria;c__Thermoleophilia : num [1:32] 0 0 0 0.000222 0 ... ## $ k__Bacteria;p__Aquificae;c__Aquificae : num [1:32] 0 0 0 0 0 0 0 0 0 0 ... ## $ k__Bacteria;p__Bacteroidetes;c__ : num [1:32] 0 0 0.000209 0 0 ... ## $ k__Bacteria;p__Bacteroidetes;c__Bacteroidia : num [1:32] 0.14 0.154 0.188 0.157 0.172 ... ## $ k__Bacteria;p__Bacteroidetes;c__Flavobacteriia : num [1:32] 0 0 0 0 0 0 0 0 0 0 ... ## $ k__Bacteria;p__Bacteroidetes;c__Sphingobacteriia : num [1:32] 0 0 0 0 0 0 0 0 0 0 ... ## $ k__Bacteria;p__Chloroflexi;c__Thermomicrobia : num [1:32] 0 0 0 0 0.000258 ... ## $ k__Bacteria;p__Cyanobacteria;c__4C0d-2 : num [1:32] 0 0 0.001879 0 0.000258 ... ## $ k__Bacteria;p__Cyanobacteria;c__Chloroplast : num [1:32] 0 0 0 0.000445 0 ... ## $ k__Bacteria;p__Elusimicrobia;c__Elusimicrobia : num [1:32] 0 0 0 0 0 0 0 0 0 0 ... ## $ k__Bacteria;p__Firmicutes;Other : num [1:32] 0 0 0 0 0 0 0 0 0 0 ... ## $ k__Bacteria;p__Firmicutes;c__Bacilli : num [1:32] 0.0276 0.0783 0.0493 0.0409 0.0147 ... ## $ k__Bacteria;p__Firmicutes;c__Clostridia : num [1:32] 0.675 0.703 0.668 0.686 0.724 ... ## [list output truncated] ## - attr(*, "spec")= ## .. cols( ## .. `#SampleID` = col_character(), ## .. Subject = col_double(), ## .. Sample = col_character(), ## .. Visit = col_double(), ## .. Timing = col_character(), ## .. Treatment = col_character(), ## .. Mixer = col_character(), ## .. Arm = col_double(), ## .. Order = col_character(), ## .. Run = col_double(), ## .. `1,3-Dihydroxyacetone_fecal` = col_double(), ## .. `2-Oxocaproate_fecal` = col_double(), ## .. `3-Phenylpropionate_fecal` = col_double(), ## .. `4-Hydroxyphenylacetate_fecal` = col_double(), ## .. Acetate_fecal = col_double(), ## .. Alanine_fecal = col_double(), ## .. Arabinose_fecal = col_double(), ## .. Arginine_fecal = col_double(), ## .. Aspartate_fecal = col_double(), ## .. Butyrate_fecal = col_double(), ## .. `DL-methionine-sulfoxide_fecal` = col_double(), ## .. Ethanol_fecal = col_double(), ## .. Formate_fecal = col_double(), ## .. Fumarate_fecal = col_double(), ## .. Galactose_fecal = col_double(), ## .. Glucose_fecal = col_double(), ## .. Glutamate_fecal = col_double(), ## .. Glycerol_fecal = col_double(), ## .. Glycine_fecal = col_double(), ## .. Hypoxanthine_fecal = col_double(), ## .. Isobutyrate_fecal = col_double(), ## .. Isoleucine_fecal = col_double(), ## .. Isovalerate_fecal = col_double(), ## .. Leucine_fecal = col_double(), ## .. Lysine_fecal = col_double(), ## .. Malonate_fecal = col_double(), ## .. Maltose_fecal = col_double(), ## .. Methanol_fecal = col_double(), ## .. Methionine_fecal = col_double(), ## .. Methylamine_fecal = col_double(), ## .. `N-Acetylglutamate_fecal` = col_double(), ## .. Nicotinate_fecal = col_double(), ## .. Ornithine_fecal = col_double(), ## .. Phenylacetate_fecal = col_double(), ## .. Phenylalanine_fecal = col_double(), ## .. Proline_fecal = col_double(), ## .. Propionate_fecal = col_double(), ## .. Ribose_fecal = col_double(), ## .. Serine_fecal = col_double(), ## .. Succinate_fecal = col_double(), ## .. Taurine_fecal = col_double(), ## .. Threonine_fecal = col_double(), ## .. Thymine_fecal = col_double(), ## .. Tryptophan_fecal = col_double(), ## .. Tyrosine_fecal = col_double(), ## .. Uracil_fecal = col_double(), ## .. Uridine_fecal = col_double(), ## .. Valerate_fecal = col_double(), ## .. Valine_fecal = col_double(), ## .. `p-Cresol_fecal` = col_double(), ## .. LinkerPrimerSequence = col_character(), ## .. `Unassigned;Other` = col_double(), ## .. `k__Archaea;p__Euryarchaeota` = col_double(), ## .. `k__Bacteria;p__Acidobacteria` = col_double(), ## .. `k__Bacteria;p__Actinobacteria` = col_double(), ## .. `k__Bacteria;p__Aquificae` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes` = col_double(), ## .. `k__Bacteria;p__Chloroflexi` = col_double(), ## .. `k__Bacteria;p__Cyanobacteria` = col_double(), ## .. `k__Bacteria;p__Elusimicrobia` = col_double(), ## .. `k__Bacteria;p__Firmicutes` = col_double(), ## .. `k__Bacteria;p__Fusobacteria` = col_double(), ## .. `k__Bacteria;p__Lentisphaerae` = col_double(), ## .. `k__Bacteria;p__Proteobacteria` = col_double(), ## .. `k__Bacteria;p__Spirochaetes` = col_double(), ## .. `k__Bacteria;p__Synergistetes` = col_double(), ## .. `k__Bacteria;p__TM7` = col_double(), ## .. `k__Bacteria;p__Tenericutes` = col_double(), ## .. `k__Bacteria;p__Verrucomicrobia` = col_double(), ## .. `k__Bacteria;p__[Thermi]` = col_double(), ## .. `Unassigned;Other;Other` = col_double(), ## .. `k__Archaea;p__Euryarchaeota;c__Methanobacteria` = col_double(), ## .. `k__Archaea;p__Euryarchaeota;c__Thermoplasmata` = col_double(), ## .. `k__Bacteria;p__Acidobacteria;c__[Chloracidobacteria]` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Coriobacteriia` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Thermoleophilia` = col_double(), ## .. `k__Bacteria;p__Aquificae;c__Aquificae` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Flavobacteriia` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Sphingobacteriia` = col_double(), ## .. `k__Bacteria;p__Chloroflexi;c__Thermomicrobia` = col_double(), ## .. `k__Bacteria;p__Cyanobacteria;c__4C0d-2` = col_double(), ## .. `k__Bacteria;p__Cyanobacteria;c__Chloroplast` = col_double(), ## .. `k__Bacteria;p__Elusimicrobia;c__Elusimicrobia` = col_double(), ## .. `k__Bacteria;p__Firmicutes;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Erysipelotrichi` = col_double(), ## .. `k__Bacteria;p__Fusobacteria;c__Fusobacteriia` = col_double(), ## .. `k__Bacteria;p__Lentisphaerae;c__[Lentisphaeria]` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Betaproteobacteria` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria` = col_double(), ## .. `k__Bacteria;p__Spirochaetes;c__Spirochaetes` = col_double(), ## .. `k__Bacteria;p__Synergistetes;c__Synergistia` = col_double(), ## .. `k__Bacteria;p__TM7;c__TM7-3` = col_double(), ## .. `k__Bacteria;p__Tenericutes;c__Mollicutes` = col_double(), ## .. `k__Bacteria;p__Tenericutes;c__RF3` = col_double(), ## .. `k__Bacteria;p__Verrucomicrobia;c__Opitutae` = col_double(), ## .. `k__Bacteria;p__Verrucomicrobia;c__Verrucomicrobiae` = col_double(), ## .. `k__Bacteria;p__[Thermi];c__Deinococci` = col_double(), ## .. `Unassigned;Other;Other;Other` = col_double(), ## .. `k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales` = col_double(), ## .. `k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__E2` = col_double(), ## .. `k__Bacteria;p__Acidobacteria;c__[Chloracidobacteria];o__RB41` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Bifidobacteriales` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Thermoleophilia;o__Solirubrobacterales` = col_double(), ## .. `k__Bacteria;p__Aquificae;c__Aquificae;o__Aquificales` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__;o__` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Flavobacteriia;o__Flavobacteriales` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Sphingobacteriia;o__Sphingobacteriales` = col_double(), ## .. `k__Bacteria;p__Chloroflexi;c__Thermomicrobia;o__JG30-KF-CM45` = col_double(), ## .. `k__Bacteria;p__Cyanobacteria;c__4C0d-2;o__YS2` = col_double(), ## .. `k__Bacteria;p__Cyanobacteria;c__Chloroplast;o__Streptophyta` = col_double(), ## .. `k__Bacteria;p__Elusimicrobia;c__Elusimicrobia;o__Elusimicrobiales` = col_double(), ## .. `k__Bacteria;p__Firmicutes;Other;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Gemellales` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales` = col_double(), ## .. `k__Bacteria;p__Fusobacteria;c__Fusobacteriia;o__Fusobacteriales` = col_double(), ## .. `k__Bacteria;p__Lentisphaerae;c__[Lentisphaeria];o__Victivallales` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Neisseriales` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Rhodocyclales` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Myxococcales` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Aeromonadales` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Alteromonadales` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales` = col_double(), ## .. `k__Bacteria;p__Spirochaetes;c__Spirochaetes;o__Spirochaetales` = col_double(), ## .. `k__Bacteria;p__Synergistetes;c__Synergistia;o__Synergistales` = col_double(), ## .. `k__Bacteria;p__TM7;c__TM7-3;o__` = col_double(), ## .. `k__Bacteria;p__TM7;c__TM7-3;o__CW040` = col_double(), ## .. `k__Bacteria;p__Tenericutes;c__Mollicutes;o__Anaeroplasmatales` = col_double(), ## .. `k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39` = col_double(), ## .. `k__Bacteria;p__Tenericutes;c__RF3;o__ML615J-28` = col_double(), ## .. `k__Bacteria;p__Verrucomicrobia;c__Opitutae;o__[Cerasicoccales]` = col_double(), ## .. `k__Bacteria;p__Verrucomicrobia;c__Verrucomicrobiae;o__Verrucomicrobiales` = col_double(), ## .. `k__Bacteria;p__[Thermi];c__Deinococci;o__Thermales` = col_double(), ## .. `Unassigned;Other;Other;Other;Other` = col_double(), ## .. `k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae` = col_double(), ## .. `k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__E2;f__[Methanomassiliicoccaceae]` = col_double(), ## .. `k__Bacteria;p__Acidobacteria;c__[Chloracidobacteria];o__RB41;f__` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Actinomycetaceae` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Brevibacteriaceae` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Corynebacteriaceae` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Dermabacteraceae` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Intrasporangiaceae` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Micrococcaceae` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Micromonosporaceae` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Propionibacteriaceae` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Bifidobacteriales;f__Bifidobacteriaceae` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Thermoleophilia;o__Solirubrobacterales;f__` = col_double(), ## .. `k__Bacteria;p__Aquificae;c__Aquificae;o__Aquificales;f__Aquificaceae` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__;o__;f__` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;Other` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__S24-7` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Barnesiellaceae]` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Odoribacteraceae]` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Paraprevotellaceae]` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Flavobacteriia;o__Flavobacteriales;f__Flavobacteriaceae` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Flavobacteriia;o__Flavobacteriales;f__[Weeksellaceae]` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Sphingobacteriia;o__Sphingobacteriales;f__Sphingobacteriaceae` = col_double(), ## .. `k__Bacteria;p__Chloroflexi;c__Thermomicrobia;o__JG30-KF-CM45;f__` = col_double(), ## .. `k__Bacteria;p__Cyanobacteria;c__4C0d-2;o__YS2;f__` = col_double(), ## .. `k__Bacteria;p__Cyanobacteria;c__Chloroplast;o__Streptophyta;f__` = col_double(), ## .. `k__Bacteria;p__Elusimicrobia;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;Other;Other;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;Other;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Listeriaceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Paenibacillaceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Planococcaceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Gemellales;f__Gemellaceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Leuconostocaceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales;f__Turicibacteraceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Christensenellaceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Dehalobacteriaceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__EtOH8` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Eubacteriaceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Gracilibacteraceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptococcaceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptostreptococcaceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__[Mogibacteriaceae]` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__[Tissierellaceae]` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae` = col_double(), ## .. `k__Bacteria;p__Fusobacteria;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae` = col_double(), ## .. `k__Bacteria;p__Lentisphaerae;c__[Lentisphaeria];o__Victivallales;f__Victivallaceae` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aurantimonadaceae` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__mitochondria` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Alcaligenaceae` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Burkholderiaceae` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Comamonadaceae` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Oxalobacteraceae` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Neisseriales;f__Neisseriaceae` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Rhodocyclales;f__Rhodocyclaceae` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Myxococcales;f__` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Campylobacteraceae` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Aeromonadales;f__Succinivibrionaceae` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Alteromonadales;f__Alteromonadaceae` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Alteromonadales;f__Shewanellaceae` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Alteromonadales;f__[Chromatiaceae]` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales;f__Pasteurellaceae` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae` = col_double(), ## .. `k__Bacteria;p__Spirochaetes;c__Spirochaetes;o__Spirochaetales;f__Spirochaetaceae` = col_double(), ## .. `k__Bacteria;p__Synergistetes;c__Synergistia;o__Synergistales;f__Synergistaceae` = col_double(), ## .. `k__Bacteria;p__TM7;c__TM7-3;o__;f__` = col_double(), ## .. `k__Bacteria;p__TM7;c__TM7-3;o__CW040;f__F16` = col_double(), ## .. `k__Bacteria;p__Tenericutes;c__Mollicutes;o__Anaeroplasmatales;f__Anaeroplasmataceae` = col_double(), ## .. `k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39;f__` = col_double(), ## .. `k__Bacteria;p__Tenericutes;c__RF3;o__ML615J-28;f__` = col_double(), ## .. `k__Bacteria;p__Verrucomicrobia;c__Opitutae;o__[Cerasicoccales];f__[Cerasicoccaceae]` = col_double(), ## .. `k__Bacteria;p__Verrucomicrobia;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae` = col_double(), ## .. `k__Bacteria;p__[Thermi];c__Deinococci;o__Thermales;f__Thermaceae` = col_double(), ## .. `Unassigned;Other;Other;Other;Other;Other` = col_double(), ## .. `k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter` = col_double(), ## .. `k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__E2;f__[Methanomassiliicoccaceae];g__` = col_double(), ## .. `k__Bacteria;p__Acidobacteria;c__[Chloracidobacteria];o__RB41;f__;g__` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Actinomycetaceae;g__` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Actinomycetaceae;g__Varibaculum` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Corynebacteriaceae;g__Corynebacterium` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Intrasporangiaceae;g__` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Micrococcaceae;g__Rothia` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Micromonosporaceae;Other` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Actinomycetales;f__Propionibacteriaceae;g__` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Bifidobacteriales;f__Bifidobacteriaceae;Other` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Bifidobacteriales;f__Bifidobacteriaceae;g__` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Bifidobacteriales;f__Bifidobacteriaceae;g__Bifidobacterium` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Adlercreutzia` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Atopobium` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Eggerthella` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Slackia` = col_double(), ## .. `k__Bacteria;p__Actinobacteria;c__Thermoleophilia;o__Solirubrobacterales;f__;g__` = col_double(), ## .. `k__Bacteria;p__Aquificae;c__Aquificae;o__Aquificales;f__Aquificaceae;g__` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__;o__;f__;g__` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;Other;Other` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__;g__` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Parabacteroides` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__Porphyromonas` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;Other` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__AF12` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__S24-7;g__` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Barnesiellaceae];g__` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Odoribacteraceae];g__Butyricimonas` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Odoribacteraceae];g__Odoribacter` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Paraprevotellaceae];g__` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Paraprevotellaceae];g__CF231` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Paraprevotellaceae];g__Paraprevotella` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Paraprevotellaceae];g__YRC22` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Paraprevotellaceae];g__[Prevotella]` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Flavobacteriia;o__Flavobacteriales;f__Flavobacteriaceae;Other` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Flavobacteriia;o__Flavobacteriales;f__[Weeksellaceae];g__` = col_double(), ## .. `k__Bacteria;p__Bacteroidetes;c__Sphingobacteriia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter` = col_double(), ## .. `k__Bacteria;p__Chloroflexi;c__Thermomicrobia;o__JG30-KF-CM45;f__;g__` = col_double(), ## .. `k__Bacteria;p__Cyanobacteria;c__4C0d-2;o__YS2;f__;g__` = col_double(), ## .. `k__Bacteria;p__Cyanobacteria;c__Chloroplast;o__Streptophyta;f__;g__` = col_double(), ## .. `k__Bacteria;p__Elusimicrobia;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__` = col_double(), ## .. `k__Bacteria;p__Elusimicrobia;c__Elusimicrobia;o__Elusimicrobiales;f__Elusimicrobiaceae;g__Elusimicrobium` = col_double(), ## .. `k__Bacteria;p__Firmicutes;Other;Other;Other;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;Other;Other;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;Other;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__;g__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Anoxybacillus` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Geobacillus` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Listeriaceae;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Paenibacillaceae;g__Cohnella` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Paenibacillaceae;g__Paenibacillus` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Planococcaceae;g__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Planococcaceae;g__Lysinibacillus` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Planococcaceae;g__Sporosarcina` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae;g__Jeotgalicoccus` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae;g__Staphylococcus` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Gemellales;f__Gemellaceae;g__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Gemellales;f__Gemellaceae;g__Gemella` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;Other;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__;g__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Facklamia` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Granulicatella` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Vagococcus` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Leuconostocaceae;g__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Leuconostocaceae;g__Leuconostoc` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales;f__Turicibacteraceae;g__Turicibacter` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;Other;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__;g__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Christensenellaceae;g__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Christensenellaceae;g__Christensenella` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Caloramator` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__SMB53` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Sarcina` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Dehalobacteriaceae;g__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Dehalobacteriaceae;g__Dehalobacterium` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__EtOH8;g__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Eubacteriaceae;g__Anaerofustis` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Eubacteriaceae;g__Pseudoramibacter_Eubacterium` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Gracilibacteraceae;g__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Anaerostipes` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Blautia` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Butyrivibrio` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Clostridium` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Coprococcus` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Dorea` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Epulopiscium` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnobacterium` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnospira` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Pseudobutyrivibrio` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__[Ruminococcus]` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptococcaceae;g__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptococcaceae;g__Desulfitobacter` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptococcaceae;g__Peptococcus` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptococcaceae;g__rc4-4` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptostreptococcaceae;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptostreptococcaceae;g__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptostreptococcaceae;g__Peptostreptococcus` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;Other` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Anaerotruncus` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Butyricicoccus` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Faecalibacterium` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Oscillospira` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Ruminococcus` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Acidaminococcus` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Anaerovibrio` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Dialister` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Megamonas` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Megasphaera` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Mitsuokella` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Phascolarctobacterium` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Succiniclasticum` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Veillonellaceae;g__Veillonella` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__[Mogibacteriaceae];g__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__[Mogibacteriaceae];g__Mogibacterium` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__[Tissierellaceae];g__Anaerococcus` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__[Tissierellaceae];g__Finegoldia` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__[Tissierellaceae];g__Parvimonas` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__[Tissierellaceae];g__Tissierella_Soehngenia` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__[Tissierellaceae];g__ph2` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Allobaculum` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Catenibacterium` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Coprobacillus` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemania` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__PSB-M-3` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Sharpea` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__[Eubacterium]` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__cc_115` = col_double(), ## .. `k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__p-75-a5` = col_double(), ## .. `k__Bacteria;p__Fusobacteria;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Cetobacterium` = col_double(), ## .. `k__Bacteria;p__Fusobacteria;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium` = col_double(), ## .. `k__Bacteria;p__Lentisphaerae;c__[Lentisphaeria];o__Victivallales;f__Victivallaceae;g__` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__;g__` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aurantimonadaceae;g__` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;Other` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__mitochondria;Other` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Alcaligenaceae;g__` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Alcaligenaceae;g__Sutterella` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lautropia` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Comamonadaceae;g__` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Comamonadaceae;g__Comamonas` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Comamonadaceae;g__Delftia` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Oxalobacteraceae;g__` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Neisseriales;f__Neisseriaceae;Other` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Neisseriales;f__Neisseriaceae;g__` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Rhodocyclales;f__Rhodocyclaceae;Other` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Bilophila` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria;o__Myxococcales;f__;g__` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae;g__` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Flexispira` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Aeromonadales;f__Succinivibrionaceae;g__` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Alteromonadales;f__Alteromonadaceae;g__unclassified` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Alteromonadales;f__Shewanellaceae;g__Shewanella` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Alteromonadales;f__[Chromatiaceae];g__Rheinheimera` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;Other` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__Escherichia` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__Klebsiella` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__Morganella` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__Proteus` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;g__Serratia` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales;f__Pasteurellaceae;Other` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales;f__Pasteurellaceae;g__Actinobacillus` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales;f__Pasteurellaceae;g__Aggregatibacter` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pasteurellales;f__Pasteurellaceae;g__Haemophilus` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas` = col_double(), ## .. `k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__` = col_double(), ## .. `k__Bacteria;p__Spirochaetes;c__Spirochaetes;o__Spirochaetales;f__Spirochaetaceae;g__Treponema` = col_double(), ## .. `k__Bacteria;p__Synergistetes;c__Synergistia;o__Synergistales;f__Synergistaceae;Other` = col_double(), ## .. `k__Bacteria;p__TM7;c__TM7-3;o__;f__;g__` = col_double(), ## .. `k__Bacteria;p__TM7;c__TM7-3;o__CW040;f__F16;g__` = col_double(), ## .. `k__Bacteria;p__Tenericutes;c__Mollicutes;o__Anaeroplasmatales;f__Anaeroplasmataceae;g__` = col_double(), ## .. `k__Bacteria;p__Tenericutes;c__Mollicutes;o__Anaeroplasmatales;f__Anaeroplasmataceae;g__Anaeroplasma` = col_double(), ## .. `k__Bacteria;p__Tenericutes;c__Mollicutes;o__RF39;f__;g__` = col_double(), ## .. `k__Bacteria;p__Tenericutes;c__RF3;o__ML615J-28;f__;g__` = col_double(), ## .. `k__Bacteria;p__Verrucomicrobia;c__Opitutae;o__[Cerasicoccales];f__[Cerasicoccaceae];g__` = col_double(), ## .. `k__Bacteria;p__Verrucomicrobia;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Akkermansia` = col_double(), ## .. `k__Bacteria;p__[Thermi];c__Deinococci;o__Thermales;f__Thermaceae;g__Meiothermu_` = col_double(), ## .. `Initial GI` = col_character(), ## .. `Initial IBS` = col_character(), ## .. `Overall Pre Improvement Q` = col_character(), ## .. `Overall Syn Improvement Q` = col_character(), ## .. `Overall Pre Improvement C` = col_character(), ## .. `Overall Syn Improvement C` = col_character(), ## .. `Diarrhea Only V1` = col_character(), ## .. `Improved DO PostPre` = col_character(), ## .. `Improved DO PostSyn` = col_character(), ## .. `Initial Pain` = col_character(), ## .. `Improved Pain PostPre` = col_character(), ## .. `Improved Pain PostSyn` = col_character(), ## .. `Novel Foods Overall` = col_character(), ## .. `2-Hydroxybutyrate_serum` = col_double(), ## .. `2-Hydroxyisovalerate_serum` = col_double(), ## .. `2-Oxoglutarate_serum` = col_double(), ## .. `3-Hydroxybutyrate_serum` = col_double(), ## .. `3-Hydroxyisobutyrate_serum` = col_double(), ## .. Acetate_serum = col_double(), ## .. Acetoacetate_serum = col_double(), ## .. Acetone_serum = col_double(), ## .. Alanine_serum = col_double(), ## .. Ascorbate_serum = col_double(), ## .. Asparagine_serum = col_double(), ## .. Betaine_serum = col_double(), ## .. Carnitine_serum = col_double(), ## .. Choline_serum = col_double(), ## .. Creatine_serum = col_double(), ## .. Creatinine_serum = col_double(), ## .. Ethanol_serum = col_double(), ## .. Formate_serum = col_double(), ## .. Glucose_serum = col_double(), ## .. Glutamate_serum = col_double(), ## .. Glutamine_serum = col_double(), ## .. Glycine_serum = col_double(), ## .. Isoleucine_serum = col_double(), ## .. Lactate_serum = col_double(), ## .. Leucine_serum = col_double(), ## .. Lysine_serum = col_double(), ## .. Mannose_serum = col_double(), ## .. Methionine_serum = col_double(), ## .. Ornithine_serum = col_double(), ## .. Phenylalanine_serum = col_double(), ## .. Proline_serum = col_double(), ## .. Pyruvate_serum = col_double(), ## .. Serine_serum = col_double(), ## .. Taurine_serum = col_double(), ## .. Threonine_serum = col_double(), ## .. Tyrosine_serum = col_double(), ## .. Urea_serum = col_double(), ## .. Valine_serum = col_double(), ## .. `1,6-Anhydro-β-D-glucose_urine` = col_double(), ## .. `1-Methylnicotinamide_urine` = col_double(), ## .. `2-Aminobutyrate_urine` = col_double(), ## .. `2-Furoylglycine_urine` = col_double(), ## .. `2-Hydroxyisobutyrate_urine` = col_double(), ## .. `2-Oxoglutarate_urine` = col_double(), ## .. `2-Oxoisocaproate_urine` = col_double(), ## .. `3-Aminoisobutyrate_urine` = col_double(), ## .. `3-Hydroxy-3-methylglutarate_urine` = col_double(), ## .. `3-Hydroxyisobutyrate_urine` = col_double(), ## .. `3-Hydroxyisovalerate_urine` = col_double(), ## .. `3-Hydroxyphenylacetate_urine` = col_double(), ## .. `3-Indoxylsulfate_urine` = col_double(), ## .. `4-Hydroxyphenylacetate_urine` = col_double(), ## .. `4-Hydroxyphenyllactate_urine` = col_double(), ## .. Acetate_urine = col_double(), ## .. Alanine_urine = col_double(), ## .. Allantoin_urine = col_double(), ## .. Arabinose_urine = col_double(), ## .. Ascorbate_urine = col_double(), ## .. Asparagine_urine = col_double(), ## .. Betaine_urine = col_double(), ## .. Choline_urine = col_double(), ## .. Citrate_urine = col_double(), ## .. Creatine_urine = col_double(), ## .. Creatinine_urine = col_double(), ## .. Dimethylamine_urine = col_double(), ## .. Formate_urine = col_double(), ## .. Fructose_urine = col_double(), ## .. Fucose_urine = col_double(), ## .. Galactose_urine = col_double(), ## .. Glucose_urine = col_double(), ## .. Glutamine_urine = col_double(), ## .. Glycerol_urine = col_double(), ## .. Glycine_urine = col_double(), ## .. Glycolate_urine = col_double(), ## .. Hippurate_urine = col_double(), ## .. Histidine_urine = col_double(), ## .. Hypoxanthine_urine = col_double(), ## .. Isobutyrate_urine = col_double(), ## .. Isoleucine_urine = col_double(), ## .. Isopropanol_urine = col_double(), ## .. Lactate_urine = col_double(), ## .. Leucine_urine = col_double(), ## .. Mannitol_urine = col_double(), ## .. Methylguanidine_urine = col_double(), ## .. Methylsuccinate_urine = col_double(), ## .. Pantothenate_urine = col_double(), ## .. Phenylalanine_urine = col_double(), ## .. `Propylene glycol_urine` = col_double(), ## .. Quinolinate_urine = col_double(), ## .. Serine_urine = col_double(), ## .. Succinate_urine = col_double(), ## .. Sucrose_urine = col_double(), ## .. Taurine_urine = col_double(), ## .. Threonine_urine = col_double(), ## .. Trigonelline_urine = col_double(), ## .. `Trimethylamine N-oxide_urine` = col_double(), ## .. Tryptophan_urine = col_double(), ## .. Tyrosine_urine = col_double(), ## .. Urea_urine = col_double(), ## .. Valine_urine = col_double(), ## .. Xylose_urine = col_double(), ## .. `cis-Aconitate_urine` = col_double(), ## .. `sn-Glycero-3-phosphocholine_urine` = col_double(), ## .. `trans-Aconitate_urine` = col_double(), ## .. `π-Methylhistidine_urine` = col_double(), ## .. IL13_CD4 = col_double(), ## .. IL13_B7 = col_double(), ## .. IL10_CD4 = col_double(), ## .. IL10_B7 = col_double(), ## .. LAP_M = col_double(), ## .. LAP_PMA = col_double(), ## .. CD25_M = col_double(), ## .. CD25_PMA = col_double(), ## .. IFNg_CD4 = col_double(), ## .. IFNg_B74 = col_double(), ## .. IFNg_CD8 = col_double(), ## .. IFNg_B78 = col_double(), ## .. IL17_CD4 = col_double(), ## .. IL17_B7 = col_double(), ## .. TNFa_CD4 = col_double(), ## .. TNFa_B74 = col_double(), ## .. TNFa_CD8 = col_double(), ## .. TNFa_B78 = col_double(), ## .. IL6_CD4 = col_double(), ## .. IL6_B7 = col_double(), ## .. P_Actinobacteria = col_double(), ## .. P_Bacteroidetes = col_double(), ## .. P_Firmicutes = col_double(), ## .. P_FBratio = col_double(), ## .. P_Proteobacteria = col_double(), ## .. C_Actinobacteria = col_double(), ## .. C_Clostridia = col_double(), ## .. C_Gammaproteobacteria = col_double(), ## .. O_Bifidobacteriales = col_double(), ## .. O_Clostridiales = col_double(), ## .. O_Enterobacteriales = col_double(), ## .. F_Bifidobacteriaceae = col_double(), ## .. F_Enterococcaceae = col_double(), ## .. F_Clostridiaceae = col_double(), ## .. F_Enterobacteriaceae = col_double(), ## .. G_Bifidobacterium = col_double(), ## .. G_Clostridium = col_double(), ## .. ABC_SS1 = col_double(), ## .. ABC_SS2 = col_double(), ## .. ABC_SS3 = col_double(), ## .. ABC_SS4 = col_double(), ## .. ABC_Total = col_double(), ## .. Pain = col_double(), ## .. Gas = col_double(), ## .. ABAS_G = col_double(), ## .. ABAS_C = col_double(), ## .. ABAS_S = col_double(), ## .. ABAS_P = col_double(), ## .. RBS_SS1 = col_double(), ## .. RBS_SS2 = col_double(), ## .. RBS_SS3 = col_double(), ## .. RBS_SS4 = col_double(), ## .. RBS_SS5 = col_double(), ## .. RBS_Total = col_double(), ## .. Q2 = col_double(), ## .. Q3 = col_double(), ## .. Dia = col_double(), ## .. Con = col_double(), ## .. Weight = col_double(), ## .. BMI = col_double(), ## .. BMIP = col_double() ## .. )
Data analysis
Exploring the data:
- Behavior vs. treatment
- GI symptoms vs. treatment
- Behavior related to microbiome
- GI symptoms related to microbiome
- Microbiome changes (PCA)
- Metabolite changes
- Immune cell population changes
Results
Change in abberant behavior after treatment
Behavioral scores of subject “202” and “212”
Gastrointestinal symptoms
Gastrointestinal symptoms
Microbiome composition
PCA of microbiomes
Aberrant behavior vs. taxa abundance
Gastrointestinal symptoms vs. taxa abundance
PCA of metabolome
Correlations of some metabolites and bacterial taxa
Immune cell phenotypes
PCA of metabolome
Correlations of some metabolites and bacterial taxa
Immune cell phenotypes
Immune cells vs. certain metabolites
Discussion
Discussion
- Improved autism symptoms
- Improved gastrointestinal symptoms
But why?
<<<<<<< HEAD- Perhaps immune cells
- Perhaps placebo?
- More subjects needed
- Longer test period
- Perhaps immune cells
- More subjects needed
- Longer test period
<<<<<<< HEAD - Perhaps immune cells (however, subject 202 and 212 do not exhibit marked changes in immune cell phenotypes) - Perhaps placebo? ======= > - Perhaps immune cells >>>>>>> ee86ad84872502b9e53762d9037d072379508495 - More subjects needed - Longer test period
>>>>>>> 829be94ab31609a3b482ad4d21269dc187d89c59 >>>>>>> e0f5a80a7a2101bdd3143daf3c76a49caf22ffe0